Difference between revisions of "Task 6 - EVfold"
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| − | For the proteins used in this practical, structures have been determined. However, in real-life projects, you often do not have protein structures only sequences. During this practical, you already predicted secondary structure elements |
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| − | correlated mutations |
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| − | local method: mutual information |
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| − | your protein |
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| − | + example P01112 (RASH_HUMAN) |
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| − | http://pfam.sanger.ac.uk/family/Ras |
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| − | calculating the evolutionary couplings |
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| − | 0. aligment (clustalw.... Pfam alignment good) Many sequences |
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| − | 1. a2m2lm.... => aligment |
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| − | 2. freecontact -> standard (installed on student computers) |
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| − | Output -> all couplings + evolutionary coupling score (last column) |
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| − | rank by score => look at distrubution, values, range |
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| − | Meaning of score unclear |
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| − | Take only scores for i+6, i.e. neighboring residues neglected, minimal 5 residues between coupled residues |
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| − | Take ranking, check for each coupled pair the actual distance in the structure. TP: distance <= 5 AA (minimal distance of all pairs of all atoms of both residues) |
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| − | EVcoupling |
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| − | Check evolutionary hot spots, i.e. relevant residues, functionally important sites. |
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| − | Take L couplings (L=length of protein sequence), sum scores for each residue. Analyze. |
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| − | (Cell paper) |
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| − | - compare to conservation, single site conservation |
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| − | EVfold.org |
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| − | create model |
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| − | choose number of contacts: |
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| − | optimum ~ 60-70% of L |
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| − | 40% of L |
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| − | 100% of L |
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| − | => RMSD will be calculated by server, if you give PDB ID |
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| − | PLM |
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